Hi Anastasia, Sorry for my slow reply. I am working with data that I only have access to intermittently. We were able to fix the problem by deleting the original files from the folder and re-running the bedpost step. The old files must have been interfering in some way.
I am hoping you can help me with a different problem I ran into. For several of our subjects, each pathway reconstruction fails and I get an error like the following for all 18 tracts: Processing pathway 16 of 18... Initializing MCMC INFO: Path from initial control points is not entirely in mask INFO: or is self-intersecting INFO: Attemping to perturb control points ERROR: Path from initial control points is not entirely in mask ERROR: or is self-intersecting ERROR: Initialization failed ERROR: Pathway reconstruction failed Done in 0.216 sec. I am able to view the FA image in native space, but when I attempt to view the FLIRT-registered FA image it's completely dark. Is there any reason you can think of that this may be happening? Thanks in advance, Kiely On Fri, Dec 23, 2011 at 2:42 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Kiely - It's strange that bepostx would create ph2samples and not > ph1samples. These are the orientation angles for the 2 anisotropic > compartments, so if there's a 2nd there should be a 1st. Have you asked > about it on the FSL list? > > a.y > > > On Thu, 22 Dec 2011, Kiely Donnelly wrote: > > Hi Everyone -- >> >> I've been having difficulty getting Tracula to run smoothly on our >> cluster. Similar to others on the listserv, the bedpost step >> was not creating the necessary files causing an error during the -path >> step. Based on previous posts, I ran bedpostx on the dmri >> directory. This initially seemed to work (I no longer received the >> message "1 slice processed" over and over), but for some reason >> the merged_ph1samples.nii.gz file is still not being created and I >> continue to run into an error when I run -path. It does create >> a merged_ph2samples.nii.gz output file. >> >> Any help would be greatly appreciated. >> >> Thanks, >> >> Kiely >> >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati
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